__init__.py

#!/usr/bin/env python## Restriction Analysis Libraries.# Copyright (C) 2004. Frederic Sohm.## This code is part of the Biopython distribution and governed by its# license. Please see the LICENSE file that should have been included# as part of this package.#"""Usage:===== >>> from Rana.fts import fts # >>> from Rana.Vector import * # Just a way to get a sequence. >>> from Bio.Seq import Seq # Use your prefer method here. >>> pbr = fts(pBR322) # >>> seq = Seq(str(pbr)) # >>> >>> from Bio.Restriction import * >>> a = Analysis(AllEnzymes, seq, linear=False) >>> b = a.blunt() >>> a.print_that() # no argument -> print all the results AasI : 2169, 2582. AatII : 4289. Acc16I : 263, 1359, 1457, 3589. ... More enzymes here. ... >>> b = a.without_site() >>> a.print_that(b, '', '\n Enzymes which do not cut pBR322.\n\n') Enzymes which do not cut pBR322. AarI AatI Acc65I AcsI AcvI AdeI AflII AgeI AhlI AleI AloI ApaI ApoI AscI AsiAI AsiSI Asp718I AspA2I AsuII AvaIII AvrII AxyI BaeI BbrPI BbvCI BclI BcuI BfrBI BfrI BglII BlnI BlpI BmgBI BmgI BplI Bpu1102I Bpu14I BsaXI Bse21I BsePI BseRI BshTI BsiWI Bsp119I Bsp120I Bsp1407I Bsp1720I Bsp19I BspT104I BspTI BsrGI BssHI BssHII Bst98I BstAUI BstBI BstEII BstPI BstSNI BstXI Bsu36I BtrI CciNI CelII Cfr42I Cfr9I CpoI Csp45I CspAI CspCI CspI DraIII DrdII Ecl136II Eco105I Eco147I Eco72I Eco81I Eco91I EcoICRI EcoO65I EcoRI EcoT22I EspI FalI FbaI FseI FunII HpaI KpnI Ksp22I KspAI KspI MabI MfeI MluI Mph1103I MspCI MssI MunI NcoI NotI NsiI NspV OliI PacI PaeR7I PasI PauI PceI Pfl23II PinAI PmaCI PmeI PmlI Ppu10I PsiI Psp124BI PspAI PspCI PspEI PspLI PspOMI PspXI PsrI RleAI Rsr2I RsrII SacI SacII SanDI SauI SbfI SciI SdaI SexAI SfiI Sfr274I Sfr303I SfuI SgfI SgrBI SlaI SmaI SmiI SnaBI SpeI SplI SrfI Sse232I Sse8387I Sse8647I SseBI SspBI SstI StuI SunI SwaI TliI UthSI Vha464I XapI XbaI XcmI XhoI XmaCI XmaI XmaJI Zsp2I >>> """from Bio.Restriction.Restriction import *
## OK can't put the following code in Bio.Restriction.__init__ unless# I put everything from Restriction in here.# or at least the RestrictionBatch class.## The reason for that is if I do that, I break the __contains__ method of# the RestrictionBatch in Restriction, which expect to find the name of# the enzymes in the locals() dictionary when evaluating string to see if# it is an enzyme.## This call for some explanations I guess:# When testing for the presence of a Restriction enzyme in a# RestrictionBatch, the user can use:## 1) a class of type 'RestrictionType'# 2) a string of the name of the enzyme (it's repr)# i.e:# >>> from Bio.Restriction import RestrictionBatch, EcoRI# >>> MyBatch = RestrictionBatch(EcoRI)# >>> #!/usr/bin/env python# >>> EcoRI in MyBatch # the class EcoRI.# True# >>># >>> 'EcoRI' in MyBatch # a string representation# True## OK, that's how it is suppose to work. And I find it quite useful.## Now if I leave the code here I got:# >>> from Bio.Restriction import RestrictionBatch, EcoRI# >>> MyBatch = RestrictionBatch(EcoRI)# >>> EcoRI in MyBatch # the class EcoRI.# True# >>> 'EcoRI' in MyBatch # a string.# False# There is 5 ways to change that:# 1) abandon the evaluation of string representation.# 2) leave the code like that and hack something in RestrictionBatch.# 3) Move back the code in Bio.Restriction.Restriction# 4) Move RestrictionBatch here.# 5) Remove Restriction.Restriction and move all the code in here## 1) no fun in that.# 2) there is a simpler way to do it.# 3) I prefer to keep all the code together.# 4) and 5) both are OK. Only a matter of preference.## So the following code has been moved back to Bio.Restricion.Restriction# For the user the results is transparent:# from Bio.Restriction import * works as before.####### The restriction enzyme classes are created dynamically when the module is### imported. Here is the magic which allow the creation of the### restriction-enzyme classes.###### The reason for the two dictionaries in Restriction_Dictionary### one for the types (which will be called pseudo-type as they really### correspond to the values that instances of RestrictionType can take)### and one for the enzymes is efficiency as the bases are evaluated### once per pseudo-type.###### However Restriction is still a very inefficient module at import. But### remember that around 660 classes (which is more or less the size of Rebase)### have to be created dynamically. However, this processing take place only### once.### This inefficiency is however largely compensated by the use of metaclass### which provide a very efficient layout for the class themselves mostly### alleviating the need of if/else loops in the class methods.###### It is essential to run Restriction with doc string optimisation (-OO switch)### as the doc string of 660 classes take a lot of processing.#####CommOnly = RestrictionBatch() # commercial enzymes##NonComm = RestrictionBatch() # not available commercially##for TYPE, (bases, enzymes) in typedict.iteritems():## ### # The keys are the pseudo-types TYPE (stored as type1, type2...)## # The names are not important and are only present to differentiate## # the keys in the dict. All the pseudo-types are in fact RestrictionType.## # These names will not be used after and the pseudo-types are not## # kept in the locals() dictionary. It is therefore impossible to## # import them.## # Now, if you have look at the dictionary, you will see that not all the## # types are present as those without corresponding enzymes have been## # removed by Dictionary_Builder().## ### # The values are tuples which contain## # as first element a tuple of bases (as string) and## # as second element the names of the enzymes.## ### # First eval the bases.## ### bases = tuple([eval(x) for x in bases])## ### # now create the particular value of RestrictionType for the classes## # in enzymes.## ### T = type.__new__(RestrictionType, 'RestrictionType', bases, {})## for k in enzymes:## ### # Now, we go through all the enzymes and assign them their type.## # enzymedict[k] contains the values of the attributes for this## # particular class (self.site, self.ovhg,....).## ### newenz = T(k, bases, enzymedict[k])## ### # we add the enzymes to the corresponding batch.## ### # No need to verify the enzyme is a RestrictionType -> add_nocheck## ### if newenz.is_comm() : CommOnly.add_nocheck(newenz)## else : NonComm.add_nocheck(newenz)###### AllEnzymes is a RestrictionBatch with all the enzymes from Rebase.#####AllEnzymes = CommOnly | NonComm###### Now, place the enzymes in locals so they can be imported.#####names = [str(x) for x in AllEnzymes]##locals().update(dict(map(None, names, AllEnzymes)))###### Limit what can be imported by from Restriction import *### Most of the classes here will never be used outside this module### (Defined,Palindromic...). It is still possible to request them specifically###### also delete the variable that are no longer needed.### #####__all__=['Analysis', 'RestrictionBatch','AllEnzymes','CommOnly','NonComm']+names##del k, x, enzymes, TYPE, bases, names